bedToBam 使用指南

bedToBam

bed 文件格式转换为bam文件利器

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bedToBam [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> > <BAM>

#示例文件: rmsk.hg18.chr21.bed

$ more rmsk.hg18.chr21.bed
chr21   9719768 9721892 ALR/Alpha   1004    +
chr21   9721905 9725582 ALR/Alpha   1010    +
chr21   9725582 9725977 L1PA3   3288    +
chr21   9726021 9729309 ALR/Alpha   1051    +
chr21   9729320 9729809 L1PA3   3897    -

#构建 GENOME文件

• 方法1

#hg18
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg18.chromInfo"  >hg18.genome
$ head hg18.genome
chrom   size
chr1    247249719
chr1_random 1663265
chr10   135374737
chr10_random    113275
chr11   134452384
chr11_random    215294
chr12   132349534
chr13   114142980
chr13_random    186858

• 方法2

$ wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.tar.gz
$ tar zvfx chromFa.tar.gz
$ cat *.fa > hg18.fa
$ rm chr*.fa
$ samtools faidx hg18.fa
$ cut -f1,2 hg18.fa.fai >hg18.genome

注: BEDtools 如果报错：Less than the req'd two fields were encountered in the genome file ；一般是由于 GENOME文件格式存在问题

#bedToBam 将bed文件转换为bam文件；

$ bedToBam -i rmsk.hg18.chr21.n.bed -g hg18.genome > rmsk.hg18.chr21.bam

#参考
BEDTools bedtobam
Biostars Question: error with bedtools slop